Automated generation of hybrid automata for multi-rigid-body mechanical systems and its application to the falsification of safety properties

© 2017 The Authors. Published by Taylor & Francis. This is an open access article available under a Creative Commons licence. The published version can be accessed at the following link on the publisher’s website: https://doi.org/10.1080/13873954.2017.1369437What if we designed a tool to automatically generate a dynamical transition system for the formal specification of mechanical systems subject to multiple impacts, contacts and discontinuous friction? Such a tool would represent an advance in the description and simulation of these complex systems. This is precisely what this paper offers: Dyverse Rigid Body Toolbox (DyverseRBT). This tool requires a sufficiently expressive computational model that can accurately describe the behaviour of the system as it evolves over time. For this purpose, we propose an alternative abstraction of multi-rigid-body (MRB) mechanical systems with multiple contacts as an extended version of the classical hybrid automaton, which we call MRB hybrid automaton. One of the chief characteristics of the MRB hybrid automaton is the inclusion of computation nodes to encode algorithms to calculate the contact forces. The computation nodes consist of a set of non-dynamical discrete locations, discrete transitions and guards between these locations, and resets on transitions. They can account for the energy transfer not explicitly considered within the rigid-body formalism. The proposed modelling framework is well suited for the automated verification of dynamical properties of realistic mechanical systems. We show this by the falsification of safety properties over the transition system generated by DyverseRBT.This work was supported by the Engineering and Physical Sciences Research Council (EPSRC) of the UK: [Grant Number EP/I001689/1] (‘DYVERSE: A New Kind of Control for Hybrid Systems’), and the Research Councils UK (RCUK): [Grant Number EP/E50048/1].Published versio

Replication of Plasmodium in reticulocytes can occur without hemozoin formation, resulting in chloroquine resistance

Most studies on malaria-parasite digestion of hemoglobin (Hb) have been performed using P. falciparum maintained in mature erythrocytes, in vitro. In this study, we examine Plasmodium Hb degradation in vivo in mice, using the parasite P. berghei, and show that it is possible to create mutant parasites lacking enzymes involved in the initial steps of Hb proteolysis. These mutants only complete development in reticulocytes and mature into both schizonts and gametocytes. Hb degradation is severely impaired and large amounts of undigested Hb remains in the reticulocyte cytoplasm and in vesicles in the parasite. The mutants produce little or no hemozoin (Hz), the detoxification by-product of Hb degradation. Further, they are resistant to chloroquine, an antimalarial drug that interferes with Hz formation, but their sensitivity to artesunate, also thought to be dependent on Hb degradation, is retained. Survival in reticulocytes with reduced or absent Hb digestion may imply a novel mechanism of drug resistance. These findings have implications for drug development against human-malaria parasites, such as P. vivax and P. ovale, which develop inside reticulocytes

Size Doesn't Matter: Towards a More Inclusive Philosophy of Biology

notes: As the primary author, O’Malley drafted the paper, and gathered and analysed data (scientific papers and talks). Conceptual analysis was conducted by both authors.publication-status: Publishedtypes: ArticlePhilosophers of biology, along with everyone else, generally perceive life to fall into two broad categories, the microbes and macrobes, and then pay most of their attention to the latter. ‘Macrobe’ is the word we propose for larger life forms, and we use it as part of an argument for microbial equality. We suggest that taking more notice of microbes – the dominant life form on the planet, both now and throughout evolutionary history – will transform some of the philosophy of biology’s standard ideas on ontology, evolution, taxonomy and biodiversity. We set out a number of recent developments in microbiology – including biofilm formation, chemotaxis, quorum sensing and gene transfer – that highlight microbial capacities for cooperation and communication and break down conventional thinking that microbes are solely or primarily single-celled organisms. These insights also bring new perspectives to the levels of selection debate, as well as to discussions of the evolution and nature of multicellularity, and to neo-Darwinian understandings of evolutionary mechanisms. We show how these revisions lead to further complications for microbial classification and the philosophies of systematics and biodiversity. Incorporating microbial insights into the philosophy of biology will challenge many of its assumptions, but also give greater scope and depth to its investigations

A sensitive method for the determination of gold and palladium based on dispersive liquid-liquid microextraction combined with flame atomic absorption spectrometric determination using N-(6-morpholin-4-ylpyridin-3-yl)-N '-phenylthiourea

Soylak, Mustafa/0000-0002-1017-0244WOS: 000369515500005A new method for the determination of gold and palladium was developed by dispersive liquid-liquid microextraction separation-preconcentration and flame atomic absorption spectrometry detection. In the proposed approach, N-(6-morpholin-4-ylpyridin-3-yl)-N'-phenylthiourea (MPPT) was synthesized as a complexing agent. The complexation ability of the MPPT was explored by examining the effect of a series of heavy metal ions, including Mn2+, Pd2+, Ni2+, Cd2+, Co2+, Cu2+, Au3+, Pb2+, Zn2+ and Fe3+, using the DLLME procedure. The MPPT exhibited pronounced selectivity toward Pd2+ and Au3+ ions at different pH levels. Factors influencing the extraction efficiency and complex formation were examined, i.e. the pH of the sample solution, the concentration of the chelating agent, the extraction and dispersive solvent type and volume, the sample volume, and foreign ions, etc. Optimal conditions for quantitative recoveries were pH 5.5 for gold and pH 1.5 for palladium, 125 mu L of % 0.4 MPPT, 1200 mu L of methanol and 125 mu L of carbon tetrachloride. The presented method showed a good linearity within a range of 30-230 and 25-200 mu g L-1 with the detection limits of 1.75 and 1.65 mu g L-1 for Au and Pd, respectively. The relative standard deviation (RSD) was below 2.8% at 50 mu g L-1 for both ions (n = 10). The developed method was simple, fast, cost efficient, and sensitive for the extraction and preconcentration of gold and palladium in samples of liquids (sea, stream water) and solids (stream sediment, ores, and electronic waste).Unit of the Scientific Research Projects of Karadeniz Technical University [1223]Financial support of the Unit of the Scientific Research Projects of Karadeniz Technical University (Project no: 1223) is gratefully acknowledged

Axonal Buckling Following Stretch Injury

Diffuse brain injury is caused by rapid rotation of the head, and causes strain injury to tissue throughout the brain. Following strain injury axons exhibit delayed recovery, showing regional buckling behavior immediately after stretch and returning to their original appearance over an extended period of time. This axonal buckling is hypothesized to occur as a result of localized stretching within the axon: Rapid strain causes mechanical damage to microtubules, increasing the effective length of axons. This damage is repaired gradually returning the axon to its initial length. Here, we test the hypothesis that localized stretching is a possible explanation for the regional buckling behavior. An elongated region of axon is modeled as an Euler beam on an elastic foundation, where the foundation represents the surrounding brain tissue, which consists of glial cells and extracellular matrix. After stretch the elastic foundation returns immediately to its pre-stretch length, while the axon is initially elongated and returns to its original length over a longer period of time. The model exhibits solutions similar to those observed experimentally in post-stretch axons, with undulations that have a similar wavelength and amplitude